Mass Effect: Extinction
by Scorp Stanton
Summary: Commander Shepard's actions, while done to safeguard the Galaxy, have resulted in Galaxy-wide chaos. Now, with the Reapers closing in, Shepard must unite the Galaxy's waring factions if she has any hope of stopping them. Reviews/Comments/Critiques welcome
1. Chapter 1: Pickup

**Mass Effect: Extinction**

_Author's Note: This is not a sequel to __Mass Effect 2.5__. Though the Shepard involved does share a name and backstory, the events of Mass Effect 2 played out __differently, as will be revealed through the story._

**Chapter 1: Pickup**

"Normandy, this is the SSV Orizaba. Prepare to be boarded."

The Orizaba aligned itself with the Normandy. A corridor extended from the Yukon's airlock until it formed a pressure-tight seal with the Normandy's.

Onboard the Normandy, a single soldier stood facing the airlock. She had deep red hair pulled back into a ponytail. Her skin looked slightly tanned, though it was her natural skin tone. There was the hint of freckles below her bright green eyes. Those eyes flicked back and forth from the cockpit to the CIC, but other than her, the ship was deserted.

The airlock opened with a hiss. Four alliance soldiers filed out, taking their positions at the four corners of Normandy's entryway. Once they were in place, a fifth man emerged.

He wore an Admiral's uniform. His facial hair was nearly white and his face was wrinkled with age. A scar, his most prominent feature, extended from just below his right eye down to his upper lip. He faced the soldier and offered a salute.

"Admiral Hackett," The soldier returned the salute. "Welcome to the Normandy."

"Shepard," he lowered his hand. "I wish I could have come under better circumstances."

"Then I take it…"

"I am here to escort you and the Normandy to Arcturus Station. I'm sorry Shepard, but I have to place you under arrest."

Shepard's demeanor was unchanged. "If I may sir, what are the charges?"

"You're being charged with Treason, several acts of Terrorism, Conspiring with known enemies of the Alliance, and impersonating an Alliance Officer."

"Well then, did you plan to clap me in irons and tow the Normandy back, or would you just like to carry out the sentence right here and now."

The two stared at each other for nearly a full minute. Suddenly, they both burst out laughing.

"Easy men, easy," Hackett called out between breaths. The puzzled soldiers lowered their weapons. He steadied himself as Shepard's laughter trailed off. "I haven't laughed like that in years."

"I hear it's good for you," Shepard smiled, "adds years to your life."

"All kidding aside Shepard, I really do have to take you in."

"I know. I said last time we spoke that I would face the consequences of my actions when the time came. If that time is now, then so be it. It's time for the Alliance to see what I've seen."

"I suppose it's time to get underway then. Seeing as how your ship is…" he looked around, "understaffed, I'll call in some spare personnel from the Orizaba. In the meantime, let's head down to the mess. I could use a coffee."

* * *

"Here you go: Coffee, black, 2 sugars."

Shepard set the steaming mug down in front of Hackett. She sat opposite him with her own mug. The liquid inside had an odd tint to it.

"What are you drinking?"

"Oh, it's coffee too. I just added a bit of Turian cream."

Hackett nearly spit out his drink. "Turian cream!"

"I've been working on building up a tolerance for dextro-proteins. They're surprisingly sweet."

"What possible reason could you have to want a tolerance for that?"

Shepard raised an eyebrow. "How does the old saying go? 'A Gentleman never asks and a Lady never tells."

Hackett contemplated his mug for a moment before turning back. "Forget I asked," he sighed.

He stood and looked around. By this point, the personnel he requested should have arrived. "Tell me Shepard. What are you doing in the middle of the Traverse on a ship with no crew?"

Shepard took a moment to answer. She leaned back in her chair and took a sip from her mug. Finally, she spoke. "Do you remember our last conversation?" She didn't wait for an answer. "I may have agreed to stand trial, but I did not speak for my crew when I said that. Each and every one of those crew members risked their lives in the pursuit of the Collectors and I'll be damned if the Alliance thinks they can prosecute them for that."

Shepard stood, sighing. "When I received the message from you, I knew it must have been about the trial. That's why, approximately eight hours ago, I instructed my crew to leave the ship."

"That's a Risky maneuver. If you'd been wrong, you'd have been stuck out here."

Shepard looked him square in the eye. "I wasn't wrong."

Hackett could sense the double meaning in her words. He set down his mug. "Look Shepard, I want you to know that I believe you. I've been defending you since you told the Council about the Reapers. That's the reason I was sent to get you, and… that's the reason I've been barred from your trial."

"Who could bar you from anything? Aren't you a full Admiral?"

"True, I'm as high as they come, except in times like these when the military decides to set up a Fleet Admiral position."

"What do you mean by 'times like these'?"

Hackett turned, trying to face a window but finding only another wall. "You've missed some changes Shepard. Political upheaval that's sending the galaxy to crap."

"I'm not sure I follow."

"You missed an election Shepard." He turned back. "Anderson isn't the councilor anymore. Seems the endorsement that got him in is exactly what lost it for him this time around."

"Who's Councilor now?"

"Who do you think?"

"Udina," Shepard muttered through clenched teeth.

Hackett nodded. "And he's wasted no time using his influence to upset the balance Anderson has been trying to maintain. He's convinced the Alliance to appoint a Fleet Admiral, a position we haven't had since the First Contact War."

"Who got promoted?"

"Admiral Mikhailovich."

Shepard brought her hand to her forehead. "Oh god, not him."

"Those were my thoughts exactly. Mikhailovich is the worst person for this job. I read his report on the original Normandy. He came off as a bigot who valued size and quantity of vessels over newer technology and overall quality. With him in charge, we're sure to lose this war."

Shepard gave a start. "War? What war are you talking about?"

Hackett picked up his mug again, looked at it, then set it back down. "We're at war with the Batarians."

"What? When did this happen?"

"Not too long after you destroyed their colony."

Shepard hung her head. "I tried to save them. I tried to warn them, get them to evacuate the colony, but there just wasn't enough time."

"I know that Shepard," Hackett offered reassuringly. "The problem is that no one else does. Hell, that's the whole reason you're going on trial in the first place!"

"They know they can't win the war, so they're trying to find the Batarians someone to punish. Is that it?"

"In a nutshell." Hackett grabbed his mug and took another drink. It was starting to get cold.

"Maybe I shouldn't have even bothered."

"Turning yourself in was the best thing you could have done."

"I don't mean turn myself in. I mean saving their sorry asses. I've been out here, busting my ass, trying to save this Galaxy. Everyone wants to stick their fingers in their ears and pretend the Reapers aren't coming, and if I make a move to try and stop them, I get labeled a villain! Now they want to drag me off to this farce of a trial. Meanwhile, the Reapers are getting progressively closer and we're still nowhere near enough to finding a way to defeat them." She slumped down in the chair. "Makes me wonder why I even bother fighting."

"You fight because it's a fight worth fighting. Anyone can fight for the rewards or the medals; you're fighting for the future, not these political shell games." Hackett sat back down. "Don't worry about the trial. I've lined up a good advocate for you. We've set up a good line of defense, not to mention your Spectre status is still good so that should shift some weight off you."

Shepard stared at her coffee for a minute. "Do you have the details of the case?"

"I can make them available to you."

"Good. I'm not going into this blind. If they want an explanation, I'm giving them one, but I refuse to be their scapegoat." She stood and turned to leave.

"You realize Shepard that while you're onboard the Normandy, you're to remain unarmed and under guard at all times."

Shepard stopped but didn't turn around. "Then tell the guard to meet me in my quarters. If you need a place to stay, the XO's office is over there. I have a case to prepare for."


	2. Chapter 2: House Arrest

**Chapter 2: House Arrest**

_Three Days Earlier_

"You know it's a trap Miranda."

Miranda was pacing in her office, wringing her hands. This was the most nervous Shepard had ever seen her since she'd met her. "I know that Shepard, but what can I do? He has my sister!"

"I know that, but that doesn't mean you have to go back to him."

Miranda shook her head. "You don't know him like I do. No one leaves Cerberus, not alive anyway. He's found a way to bring me back and it won't be long before he finds a way for Jacob," she stopped pacing and looked Shepard in the eye, "and you."

"At least give it some more time. We can work out a plan, find some way to rescue her and keep her safe."

"We don't have that kind of time. If I don't leave today, he'll force my sister to serve out my contract. I promised her a normal life. I can't ask her to—" Miranda brought her hand up to her mouth and bit her fist.

"At least let me come with you. I can help you. Maybe we can negotiate some way to…"

Miranda cut her off with a wave of her hand, "You have to be here, on this ship when Admiral Hackett arrives. You have to convince the Alliance that the Reapers are real and that they are coming. Show them the data Liara's collected. If you're lucky, maybe they'll listen in time to take the proper precautions."

Shepard nodded. She didn't like it, but she knew what she had to do. "These last few months have been like torture, watching everybody leave. I thought for sure I'd have you with me when the time came. You've been like a sister to me Miranda, but I suppose your real sister has to come first."

Miranda grabbed her by the shoulders. "It'll be alright Shepard. I'm sure you'll see them again soon enough."

"I'll see you again too." Shepard came in for a hug. "That's a promise."

Miranda patted Shepard gently. Normally she'd be uncomfortable with this level of contact, but she'd gotten used to it with Leanna.

A few hours later, Miranda was boarding a spare transport pod.

"You take care of yourself, Miranda."

She smirked. "I always do."

* * *

_Now_

Shepard stood in the shower, the water falling on her. She felt… scared? No, not scared; not nervous either; anxious, that was the word. She felt like she was going in to battle without any support. A battle she couldn't even shoot her way out of. She had to trust that the data Liara had collected as the Shadow Broker would be enough to convince the Alliance. Miranda had thought it was enough, but…

She stopped herself. She had finished washing five minutes ago, now she was just standing there, wasting water.

She stepped out of the shower, only to find she'd forgotten to grab a towel. "Great," she said out loud. "Now I gotta deal with this crap."

She walked over to the door of her private bathroom and opened it. A very young looking soldier stood on the other side. He took one look at Shepard and quickly looked away, turning his back on her.

"So modest. What's the matter marine? Never seen a naked woman before?"

"No! I mean yes! I mean… it's just that… you…" he trailed off into something unintelligible.

"Are you just gonna keep rambling like that? 'Cause if you want to make yourself useful, you can grab me a towel."

Without speaking, he grabbed a towel off Shepard's desk and shoved it behind himself.

"A _clean_ towel marine."

"Where…"

"In the armor locker, next to my bed."

The soldier made his way to the locker. It opened, revealing a large number of clothes and armor pieces.

"Left side," Shepard shouted, "top shelf."

He had to stand on his toes, but he managed to reach a towel. He pulled it down, and two more fell with it. He started to gather them up and it looked like he was about to fold them.

"Don't worry about it; just bring me the red one."

He nodded and grabbed the red towel. He started to make his way back to the bathroom, looking down at his feet as he went.

He had just reached the small set of stairs leading to Shepard's office when she called out to him again, "Marine!"

He raised his head to look at her, only to jerk it hastily to side. His cheeks were flushed.

Shepard chuckled. "Careful, you'll give yourself whiplash."

He walked the rest of the way to the bathroom and blindly handed Shepard the towel. He then took a sentry position next to door, careful not to look at her.

Shepard toweled off her legs, arms and hair, then wrapped the towel around herself. She grabbed a ring off her desk and threaded her hair through it, securing it into a ponytail with a magnetic hair-clip. She then made her way to her bed. A small metal box sat on it.

She opened the box to find a set of contemporary Alliance fatigues inside, a gift from Hackett. She felt the material; it was rough. The sensation brought her back to her early days in the Alliance. She remembered her drill instructor, being made to re-learn how to do things she took for granted, coming to depend on her teammates.

She sighed, a sort of half smile on her face.

Of course, she'd gotten used to certain comforts over the past year. She opened her armor locker and pulled out a silk bra and panty set Kasumi had convinced her to buy on their last shopping trip together. She remembered how reluctant she'd been, both to make the purchase and go on the trip, but she hadn't regretted either.

She dropped the towel. Out of the corner of her eye, she saw the soldier whirl around. She smiled to herself as she changed into the underwear and fatigues.

She was fumbling with the clasp when she asked, "What do they call you marine?"

"Uh…"

"Is that Private or Corporal Uh?"

"Stevens. Private Second Class Chad Stevens, but everyone just calls me Chip."

Shepard had put on the pants and was working on the belt. "Why do they call you Chip?"

"Well, my dad's a marine too, Captain Rick Stevens. He was so proud of me when I enlisted, and he's never proud of anyone. He called me a chip off the old block. Since then, everyone started calling me Chip."

Shepard was lacing up her boots. "You look pretty young Chip. How old are you? 19? 20?

"18. This is my first assignment."

Shepard put on the jacket and was doing up the oddly curving side-zipper. "18? And they put you on the flagship of the Fifth Fleet your first time out? Damn, I feel sorry for you."

"Don't be. I'm out here doing what I want to do and loving every minute of it. If I die tomorrow, I'll die happy."

Shepard was fully dressed. She walked over to Chip. "That's a healthy way to look at it. You can turn around by the way, I'm fully dressed now." Chip cast a quick glance over his shoulder before turning around entirely. Shepard gave a salute. "Private Second Class Chad Stevens, I'm Lt Commander Leanna Shepard."

Chip returned the salute. "Yes, I know ma'am … uh, I mean sir."

Shepard lowered her hand and cracked a smile. "Actually, you were right the first time, though I don't mind 'sir' either, or you can just call me 'Commander' or 'Shepard'. Just don't call me by my first name."

"Too informal?"

"It's not that, it's just that no one ever pronounces it right. It's pronounced 'Lee-Ann-Uh'. Don't bother to say it if you're just gonna butcher it." Chip smiled at that. "Ah, so you do have emotions other than embarrassment. Good to know. There's hope for you yet."

* * *

An hour had passed and Shepard was hard at work on her console. She was trying to make sense of the charges against her, but it was as boring as reading one of Miranda's reports. This was exactly why she never went into law.

The main doors to the cabin opened as a man stepped in. Even before he spoke, Shepard knew who it was.

"Dismissed Private," Hackett's rough voice came from behind her. Chip nodded and exited the cabin.

Shepard closed her display. It was giving her a headache anyway. "Welcome to the Loft Admiral. I'd say pull up a chair, but I've only got the one."

"It's alright." Hackett turned his attention to the dog-tags sitting on her desk. "I see these finally found their way to you."

"Yes. Liara gave them to me."

Hackett nodded his head. "Good, good. I'm glad she was able to."

"Sir, I get the feeling you're not here for chit-chat."

Hackett shook his head. "No, you're right. It's that damned Mikhailovich. He wants me to question you before the trial."

"What about?"

"He wants the whereabouts of your squad. He said I should record you and not let you know I'm doing it so you'll be candid with me. I'm not gonna do that though."

Shepard stood, straightening her jacket as she did so. "You might as well. I'll just tell you what I can and fill in the rest with blatant lies."

Hackett chuckled. "I just meant I wasn't going to lie about recording you. Feel free to lie to about their locations like crazy though, let Mikhailovich figure things out for his own damn self."

Shepard gestured to the sitting area of her quarters. They took seats at on either side of the corner-couch. Hackett placed a recording device on the coffee table and turned it on. He then pulled out a data-pad.

"Ok, going down the list, first we have Lawson, Miranda."

"Miranda, Operative Lawson returned to Cerberus under threat, and I cannot elaborate further."

"Taylor, Jacob."

"He left with the rest of my crew. His job is to keep them safe."

"Next is the Pilot, Jeff Moreau, a.k.a. 'Joker'"

"Also left with the crew, and so did Dr. Chakwas and Yeoman Chambers so you can just skip them both."

"Dr. Mordin Solus, alias 'the Professor'"

"He left with Thane Krios. I'm not sure where they were going but they intended to find a treatment for his Kepral's Syndrome."

"Check him off too then. Next up is Garrus Vakarian."

"I'm unsure as to his location. He left about a month ago. He said something about family problems."

"How about the biotic Jack, also called 'Subject Zero'?"

"Couldn't tell you. Two months ago we docked on Omega and she disappeared. Haven't seen or heard from her since."

"What about the Krogan, Urdnot Grunt?"

"Last I heard he was headed for Tuchunka. He said he wanted to 'cash in those breeding requests.'" She smiled at the though.

"Let's see, there was also a Justicar named Samara."

"Yeah, a little before Jack left, Samara told me her vow to me was finished and her code required her to return to her duties despite her personal feelings, whatever that meant."

"There's also Zaeed Massani, formerly of the Blue Suns."

"Gone. The idiot left the ship to chase after his old partner. I'm inclined to say good riddance on that matter."

"Reports sighted you with a young woman, hooded, possibly of Japanese descent. We couldn't find a name for her though."

"Sorry, but I can neither confirm, nor deny the existence of such a woman on my ship."

Now it was Hackett's turn to crack a smile. "What about the reports of a synthetic personal assistant?"

"I'd say to those people that red sand is a hell of a drug."

Hackett tried his best not to laugh. "Ok, one more and we're done. Tali'Zorah nar Rayya vas Neema."

"Vas Normandy, actually."

"I'm sorry, what?"

"She was involved in a little legal scuffle with her people and her name was officially made Tali'Zorah vas Normandy."

"I see. I'll make a note of that. Do you happen to know her whereabouts?"

"She left, a few weeks ago. The Migrant Fleet wanted to make her an Admiral, fill her father's shoes as it were. It was a… bad day for me."

Hackett nodded, seeing the emotion in Shepard's face. "One more question, if you can."

Shepard composed herself. "Go ahead Admiral."

"There were reports that your ship was working with an AI installed on it, but our teams found no trace of it. What happened to the AI?"

"We dismantled it. An unshackled AI was too dangerous to leave running."

Hackett nodded. "Well, that's all the questions I have for you. I'll report my findings to the other Admirals." He brought the recording device up to his mouth. "Hopefully we can get this mess sorted out quickly." He hit the off switch.

The two stood and Hackett walked to the door. Shepard spoke. "Thank you for stopping by sir. It was good to talk to someone, even if it was just a bunch of questioning."

Hackett turned back and gave a half smile. "I'm sure I'll come by again Shepard. We've still got about half a day before we reach Arcturus. I can tell Stevens to wait in the hall if you want."

Shepard shook her head. "Send him in. I could use the company."

Hackett nodded. "Just between you and me, how much of what you said was on the level?"

"Honestly? Most of it."

"Then I'm very sorry. Losing people on the battlefield can be tough, but losing them to their own problems can be even worse."

Shepard couldn't think of anything else to say, so she simply nodded. The doors closed with a hiss as Hackett left.


End file.
